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Wang Y, Pan Z, Mou M, Xia W, Zhang H, Zhang H, Liu J, Zheng L, Luo Y, Zheng H, Yu X, Lian X, Zeng Z, Li Z, Zhang B, Zheng M, Li H, Hou T, Zhu F. A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder. Nucleic Acids Res 2023; 51:e110. [PMID: 37889083 PMCID: PMC10682500 DOI: 10.1093/nar/gkad929] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/01/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
RNAs play essential roles in diverse physiological and pathological processes by interacting with other molecules (RNA/protein/compound), and various computational methods are available for identifying these interactions. However, the encoding features provided by existing methods are limited and the existing tools does not offer an effective way to integrate the interacting partners. In this study, a task-specific encoding algorithm for RNAs and RNA-associated interactions was therefore developed. This new algorithm was unique in (a) realizing comprehensive RNA feature encoding by introducing a great many of novel features and (b) enabling task-specific integration of interacting partners using convolutional autoencoder-directed feature embedding. Compared with existing methods/tools, this novel algorithm demonstrated superior performances in diverse benchmark testing studies. This algorithm together with its source code could be readily accessed by all user at: https://idrblab.org/corain/ and https://github.com/idrblab/corain/.
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Affiliation(s)
- Yunxia Wang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Weiqi Xia
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Hanyu Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Jin Liu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Lingyan Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Hanqi Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Xinyuan Yu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Xichen Lian
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Zhenyu Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Bing Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Mingyue Zheng
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Honglin Li
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Polytechnic Institute, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-ZJU Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
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Su Z, Lu H, Wu Y, Li Z, Duan L. Predicting potential lncRNA biomarkers for lung cancer and neuroblastoma based on an ensemble of a deep neural network and LightGBM. Front Genet 2023; 14:1238095. [PMID: 37655066 PMCID: PMC10466784 DOI: 10.3389/fgene.2023.1238095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/19/2023] [Indexed: 09/02/2023] Open
Abstract
Introduction: Lung cancer is one of the most frequent neoplasms worldwide with approximately 2.2 million new cases and 1.8 million deaths each year. The expression levels of programmed death ligand-1 (PDL1) demonstrate a complex association with lung cancer. Neuroblastoma is a high-risk malignant tumor and is mainly involved in childhood patients. Identification of new biomarkers for these two diseases can significantly promote their diagnosis and therapy. However, in vivo experiments to discover potential biomarkers are costly and laborious. Consequently, artificial intelligence technologies, especially machine learning methods, provide a powerful avenue to find new biomarkers for various diseases. Methods: We developed a machine learning-based method named LDAenDL to detect potential long noncoding RNA (lncRNA) biomarkers for lung cancer and neuroblastoma using an ensemble of a deep neural network and LightGBM. LDAenDL first computes the Gaussian kernel similarity and functional similarity of lncRNAs and the Gaussian kernel similarity and semantic similarity of diseases to obtain their similar networks. Next, LDAenDL combines a graph convolutional network, graph attention network, and convolutional neural network to learn the biological features of the lncRNAs and diseases based on their similarity networks. Third, these features are concatenated and fed to an ensemble model composed of a deep neural network and LightGBM to find new lncRNA-disease associations (LDAs). Finally, the proposed LDAenDL method is applied to identify possible lncRNA biomarkers associated with lung cancer and neuroblastoma. Results: The experimental results show that LDAenDL computed the best AUCs of 0.8701, 107 0.8953, and 0.9110 under cross-validation on lncRNAs, diseases, and lncRNA-disease pairs on Dataset 1, respectively, and 0.9490, 0.9157, and 0.9708 on Dataset 2, respectively. Furthermore, AUPRs of 0.8903, 0.9061, and 0.9166 under three cross-validations were obtained on Dataset 1, and 0.9582, 0.9122, and 0.9743 on Dataset 2. The results demonstrate that LDAenDL significantly outperformed the other four classical LDA prediction methods (i.e., SDLDA, LDNFSGB, IPCAF, and LDASR). Case studies demonstrate that CCDC26 and IFNG-AS1 may be new biomarkers of lung cancer, SNHG3 may associate with PDL1 for lung cancer, and HOTAIR and BDNF-AS may be potential biomarkers of neuroblastoma. Conclusion: We hope that the proposed LDAenDL method can help the development of targeted therapies for these two diseases.
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Affiliation(s)
- Zhenguo Su
- Clinical Lab, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, China
| | - Huihui Lu
- Department of Thoracic Cardiovascular Surgery, Hunan Province Directly Affiliated TCM Hospital, Zhuzhou, China
| | - Yan Wu
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Zejun Li
- School of Computer Science, Hunan Institute of Technology, Hengyang, China
| | - Lian Duan
- Faculty of Pediatrics, The Chinese PLA General Hospital, Beijing, China
- Department of Pediatric Surgery, The Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
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Daneshpour MS, Akbarzadeh M, Lanjanian H, Sedaghati-Khayat B, Guity K, Masjoudi S, Zahedi AS, Moazzam-Jazi M, Bonab LNH, Shalbafan B, Asgarian S, Farhood GK, Javanrooh N, Zarkesh M, Riahi P, Moghaddas MR, Dehkordi PA, Ahmadi AD, Hosseini F, Farahani SJ, Hadaegh F, Mirmiran P, Tehrani FR, Ghanbarian A, Pasand MSFM, Amiri P, Valizadeh M, Hosseipanah F, Tohidi M, Ghasemi A, Zadeh-Vakili A, Piryaei M, Alamdari S, Khalili D, Momenan A, Barzin M, Zeinali S, Hedayati M, Azizi F. Cohort profile update: Tehran cardiometabolic genetic study. Eur J Epidemiol 2023:10.1007/s10654-023-01008-1. [PMID: 37169991 PMCID: PMC10175059 DOI: 10.1007/s10654-023-01008-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 04/13/2023] [Indexed: 05/13/2023]
Abstract
The Tehran cardiometabolic genetic study (TCGS) is a large population-based cohort study that conducts periodic follow-ups. TCGS has created a comprehensive database comprising 20,367 participants born between 1911 and 2015 selected from four main ongoing studies in a family-based longitudinal framework. The study's primary goal is to identify the potential targets for prevention and intervention for non-communicable diseases that may develop in mid-life and late life. TCGS cohort focuses on cardiovascular, endocrine, metabolic abnormalities, cancers, and some inherited diseases. Since 2017, the TCGS cohort has augmented by encoding all health-related complications, including hospitalization outcomes and self-reports according to ICD11 coding, and verifying consanguineous marriage using genetic markers. This research provides an update on the rationale and design of the study, summarizes its findings, and outlines the objectives for precision medicine.
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Affiliation(s)
- Maryam S Daneshpour
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran.
| | - Mahdi Akbarzadeh
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Hossein Lanjanian
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Bahar Sedaghati-Khayat
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Kamran Guity
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
- Faculty of Medicine, University of Iceland, School of Health Sciences, Reykjavik, Iceland
| | - Sajedeh Masjoudi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Asiyeh Sadat Zahedi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Maryam Moazzam-Jazi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Leila Najd Hassan Bonab
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Bita Shalbafan
- Clinical Research Development Center of Labbafinejad Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sara Asgarian
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Goodarz Koli Farhood
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Niloofar Javanrooh
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Maryam Zarkesh
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Parisa Riahi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Mohammad Reza Moghaddas
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Parvaneh Arbab Dehkordi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Azar Delbarpour Ahmadi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Firoozeh Hosseini
- Nutrition and Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sara Jalali Farahani
- Research Center for Social Determinants of Health, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farzad Hadaegh
- Prevention of Metabolic Disorders Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parvin Mirmiran
- Nutrition and Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fahimeh Ramezani Tehrani
- Reproductive Endocrinology Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arash Ghanbarian
- Prevention of Metabolic Disorders Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Parisa Amiri
- Research Center for Social Determinants of Health, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Valizadeh
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farhad Hosseipanah
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Tohidi
- Prevention of Metabolic Disorders Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Asghar Ghasemi
- Endocrine Physiology Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azita Zadeh-Vakili
- Endocrine Physiology Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Piryaei
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Shahram Alamdari
- Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Davood Khalili
- Prevention of Metabolic Disorders Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirabbas Momenan
- Prevention of Metabolic Disorders Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Barzin
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sirous Zeinali
- Dr. Zeinali's Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
| | - Mehdi Hedayati
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran
| | - Fereidoun Azizi
- Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box 19195-4763, Tehran, Iran.
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Naghizadeh MM, Bakhshandeh B, Noorbakhsh F, Yaghmaie M, Masoudi-Nejad A. Rewiring of miRNA-mRNA bipartite co-expression network as a novel way to understand the prostate cancer related players. Syst Biol Reprod Med 2023:1-12. [PMID: 37018429 DOI: 10.1080/19396368.2023.2187268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
The differential expression and direct targeting of mRNA by miRNA are two main logics of the traditional approach to constructing the miRNA-mRNA network. This approach, could be led to the loss of considerable information and some challenges of direct targeting. To avoid these problems, we analyzed the rewiring network and constructed two miRNA-mRNA expression bipartite networks for both normal and primary prostate cancer tissue obtained from PRAD-TCGA. We then calculated beta-coefficient of the regression-model when miR was dependent and mRNA independent for each miR and mRNA and separately in both networks. We defined the rewired edges as a significant change in the regression coefficient between normal and cancer states. The rewired nodes through multinomial distribution were defined and network from rewired edges and nodes was analyzed and enriched. Of the 306 rewired edges, 112(37%) were new, 123(40%) were lost, 44(14%) were strengthened, and 27(9%) weakened connections were discovered. The highest centrality of 106 rewired mRNAs belonged to PGM5, BOD1L1, C1S, SEPG, TMEFF2, and CSNK2A1. The highest centrality of 68 rewired miRs belonged to miR-181d, miR-4677, miR-4662a, miR-9.3, and miR-1301. SMAD and beta-catenin binding were enriched as molecular functions. The regulation was a frequently repeated concept in the biological process. Our rewiring analysis highlighted the impact of β-catenin and SMAD signaling as also some transcript factors like TGFB1I1 in prostate cancer progression. Altogether, we developed a miRNA-mRNA co-expression bipartite network to identify the hidden aspects of the prostate cancer mechanism, which traditional analysis -like differential expression- was not detect it.
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Affiliation(s)
- Mohammad Mehdi Naghizadeh
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Behnaz Bakhshandeh
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Farshid Noorbakhsh
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Marjan Yaghmaie
- Hematology, Oncology and Stem Cell Transplantation Research Center, Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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An allosteric ribozyme generator and an inverse folding ribozyme generator: Two computer programs for automated computational design of oligonucleotide-sensing allosteric hammerhead ribozymes with YES Boolean logic function based on experimentally validated algorithms. Comput Biol Med 2022; 145:105469. [DOI: 10.1016/j.compbiomed.2022.105469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 11/18/2022]
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Wu H, Liang Q, Zhang W, Zou Q, El-Latif Hesham A, Liu B. iLncDA-LTR: Identification of lncRNA-disease associations by learning to rank. Comput Biol Med 2022; 146:105605. [PMID: 35594681 DOI: 10.1016/j.compbiomed.2022.105605] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/27/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]
Abstract
Identifying the associations between lncRNAs and diseases is helpful for the treatment and diagnosis of complex diseases. The existing computational methods mainly focus on the identification of associations between known lncRNAs and known diseases. However, with the application of high-throughput sequencing in lncRNA research, more and more lncRNAs have been detected. Predicting diseases related with newly detected lncRNAs has not been fully explored. Therefore, there is an urgent need for developing powerful computational methods to predict diseases related with newly detected lncRNAs. In this paper, we propose a Learning to Rank (LTR)-based method called iLncDA-LTR to predict diseases related with newly detected lncRNAs. iLncDA-LTR treats this task as an information retrieval task. The newly detected lncRNAs and diseases are considered as queries and documents, respectively. For a given newly detected lncRNA (query), iLncDA-LTR integrates multiple relevant information into LTR for predicting candidate diseases associated with query lncRNA. Experimental results show that iLncDA-LTR outperforms the other exiting state-of-the-art predictors on independent dataset. The corresponding web server of iLncDA-LTR has been constructed as well (http://bliulab.net/iLncDA-LTR/).
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Affiliation(s)
- Hao Wu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China.
| | - Qi Liang
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China.
| | - Wenxiang Zhang
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
| | - Abd El-Latif Hesham
- Genetics Department, Faculty of Agriculture, Beni-Suef University, Beni-Suef, 62511, Egypt.
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China.
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Tuning hyperparameters of machine learning algorithms and deep neural networks using metaheuristics: A bioinformatics study on biomedical and biological cases. Comput Biol Chem 2022; 97:107619. [DOI: 10.1016/j.compbiolchem.2021.107619] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/23/2021] [Accepted: 12/17/2021] [Indexed: 12/14/2022]
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